nhppSpike: Spike rates of NHPP

In seqCBS: Copy Number Profiling using Sequencing and CBS

Description

Randomly spike the smoothed control rate of an NHPP according to the parameters.

Usage

nhppSpike(smoothRates, nSpike = 25, cptLenR = 4, cptLenMean = 10, 
  minGain = 1.5, maxGain = 10, minLoss = 0.01, maxLoss = 0.5, pGain = 0.6)

Arguments

smoothRates	The smoothed rate estimate of the control process
nSpike	Number of signal spikes
cptLenR	Parameter for signal width (parameter R of negative binomial)
cptLenMean	Parameter for signal width (mean width)
minGain	Minimal Gain relative CN
maxGain	Maximal Gain relative CN
minLoss	Minimal Loss relative CN
maxLoss	Maximal Loss relative CN
pGain	Proportion of signal regions that are CN gain.

Details

The signal width is randomly generated by negative binomial distribution with the two parameters given. The signal strength are uniformly drawn between the two limits.

Value

spikeMat	A matrix containing the actual signal spike information
caseRates	The rate of the case PP to be simulated after signal spike

Author(s)

Jeremy J. Shen

See Also

nhppSimulate

seqCBS documentation built on May 2, 2019, 9:15 a.m.